ensure temp file cleanup

Author: TomBlock

core/src/main/java/com/bc/fiduceo/util/TempFileUtils.java

@@ -70,9 +70,11 @@ public File createDir(String directoryName) throws IOException {
     }
 
     public void delete(File tempFile) {
-        deleteFileIfExists(tempFile);
+        final boolean deleted = deleteFileIfExists(tempFile);
 
-        tempFileList.remove(tempFile);
+        if (deleted) {
+            tempFileList.remove(tempFile);
+        }
     }
 
     public void cleanup() {
@@ -85,17 +87,21 @@ public void cleanup() {
         }
     }
 
-    private void deleteFileIfExists(File tempFile) {
+    private boolean deleteFileIfExists(File tempFile) {
+        boolean success = true;
         if (tempFile.isFile()) {
             if (!tempFile.delete()) {
                 FiduceoLogger.getLogger().warning("Unable to delete file: " + tempFile.getAbsolutePath());
+                success = false;
             }
         }
         if (tempFile.isDirectory()) {
             if (!FileUtils.deleteTree(tempFile)) {
                 FiduceoLogger.getLogger().warning("Unable to delete directory: " + tempFile.getAbsolutePath());
+                success = false;
             }
         }
+        return success;
     }
 
     public void keepAfterCleanup(boolean keep) {

matchup-tool/src/main/java/com/bc/fiduceo/matchup/strategy/InsituPolarOrbitingMatchupStrategy.java

@@ -178,6 +178,8 @@ public MatchupCollection createMatchupCollection(ToolContext context) throws SQL
             applyConditionsAndScreenings(matchupSet, conditionEngine, conditionEngineContext, screeningEngine, primaryReader, secondaryReaders);
         }
 
+        readerCache.close();
+
         return combineBean.matchupCollection;
     }